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Re: counting cells in Image J in an NDPI format

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Fomenky, Bridget

Re: counting cells in Image J in an NDPI format

Hi everyone,

I will like to know if it is possible to use image J to count cells (stained with Alcian blue for acidic mucins) in an NDPI format.
If so could someone tell me what to do.

Bridget

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ??????? ??????
Sent: October-11-16 2:29 AM
To: [hidden email]
Subject: Re: Cell automatic selection on bad image

Thank you for answer!
Yes, I have tried it, and it didn't work well. Though I have little experience with weka. So, since you are advising it, I'll check some manuals and will try more. Without some expert opinion it is hard to understand was it my mistake or not suitable method.

V

2016-10-10 22:24 GMT+03:00 Curtis Rueden <[hidden email]>:

> Hi Vasily,
>
> Did you try the Trainable Weka Segmentation?
>
> http://imagej.net/Trainable_Weka_Segmentation
> http://forum.imagej.net/t/analysis-of-aggregates/303/3?u=ctrueden
> http://imagej.net/Segmentation
>
> Note the following helpful comment in that forum thread: "In the
> settings, I had added the Variance and Structure features, increased
> the maximum sigma to 32, and checked Homogenize classes"
>
> I did not have time right now to try it with your data, but perhaps it
> helps you.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - http://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Mon, Oct 10, 2016 at 7:38 AM, Василий Попков <[hidden email]>
> wrote:
>
> > Good time of a day, friends and colleagues.
> > Anyone can give me some advices how (and if - maybe it will be wiser
> > not
> to
> > waste time) I can automaticly select cells (for roi manager) on such
> image?
> > For "eyes" it dosent look so bad, though yes, phase is awful,
> > thankfully fluorescent channel is ok, but it's hard to distinguish
> > cells there. But
> I
> > have tried all more or less standart methods and they all were doing
> quite
> > bad selection.
> > Or, to be more cpecific, they select almost nothing - I'll be more
> > or
> less
> > ok with "bad" selection if it will be bad selection of cells.
> > Otherwise I am going to manually select them with "cell magic wand tool".
> > Its just a bit "not clever" work.
> >
> > Thanks,
> > Vasily
> >
> > --
> > Vasily A Popkov
> > Lab.Structure and function of mitochondria A.N.Belozersky Institute
> > of Physico-Chemical Biology Moscow State University
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Vasily A Popkov
Lab.Structure and function of mitochondria A.N.Belozersky Institute of Physico-Chemical Biology Moscow State University

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Krs5

Re: counting cells in Image J in an NDPI format

Dear Bridget,

According to this list (http://www.openmicroscopy.org/site/support/bio-formats5.2/supported-formats.html) the Bio-Formats plugin can read Hamamatsu NDPI formats.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fomenky, Bridget
Sent: 11 October 2016 16:27
To: [hidden email]
Subject: Re: counting cells in Image J in an NDPI format

Hi everyone,

I will like to know if it is possible to use image J to count cells (stained with Alcian blue for acidic mucins) in an NDPI format.
If so could someone tell me what to do.

Bridget

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ??????? ??????
Sent: October-11-16 2:29 AM
To: [hidden email]
Subject: Re: Cell automatic selection on bad image

Thank you for answer!
Yes, I have tried it, and it didn't work well. Though I have little experience with weka. So, since you are advising it, I'll check some manuals and will try more. Without some expert opinion it is hard to understand was it my mistake or not suitable method.

V

2016-10-10 22:24 GMT+03:00 Curtis Rueden <[hidden email]>: